HaploC

Introduction

HaploC provides a comprehensive workflow for SNP calling, haplotype phasing, and generation of unphased and phased (i.e., haplotype-specific) Hi-C maps from Hi-C experiments. HaploC only requires Hi-C reads as input

Usage

Phasing new Hi-C data using pre-existing haplotypes, it involves all steps of HaploC, except SNP calling and haplotype inference. This can be summarized in three steps

1. Create New_hic Folder: Set up a folder named 'New_hic' with the configuration file and fastq files.
2. Link to Phased_hic: Establish a softlink from the SNP and haplotype folder in 'Phased_hic' to the 'New_hic' folder.
3. Run HaploC Steps: Execute all HaploC steps, omitting SNP calling and haplotype inference.

We provide a one line command for this process:

HaploC-tools/bin/HaploC.sh -d wk_dir

Example

HaploC-tools/bin/HaploC.sh -d demo_data

Output Structure

The phased Hi-C maps are stored under:

wk_dir/mega/HapCut/hic_phased/
|-- all_chrs.opt.mat.hic
|-- all_chrs.opt.pat.hic
|-- all_chrs.opt.n_impute.mat.hic
|-- all_chrs.opt.n_impute.pat.hic
|-- all_chrs.opt.inter.mat.hic
|-- all_chrs.opt.inter.pat.hic
|-- all_chrs.opt.inter.switch.mat.hic
|-- all_chrs.opt.inter.switch.pat.hic
|-- generated_random_mix

The unphased mega Hi-C maps is stored under (same as the output of Juicer pipeline):

wk_dir/mega/aligned/
|-- inter.hic
|-- inter.txt
|-- inter_hists.m

File description:

Name	Description
inter.hic	unphased mega Hi-C map
all_chrs.opt.mat.hic	phased Hi-C map of hap1
all_chrs.opt.pat.hic	phased Hi-C map of hap1
all_chrs.opt.n_impute.mat.hic	phased Hi-C map of hap1, without imputation
all_chrs.opt.n_impute.pat.hic	phased Hi-C map of hap1, without imputation
all_chrs.opt.inter.mat.hic	phased Hi-C map of hap1 x hap1, inter-chr Hi-C map
all_chrs.opt.inter.pat.hic	phased Hi-C map of hap2 x hap2, inter-chr Hi-C map
all_chrs.opt.inter.switch.mat.hic	phased Hi-C map of hap1 x hap2, inter-chr Hi-C map
all_chrs.opt.inter.switch.pat.hic	phased Hi-C map of hap2 x hap1, inter-chr Hi-C map
generated_random_mix	random "phased" Hi-C map